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Hello Alex: Is it possible that the PC and the server run different versions of affy package? looking at sessionInfo() output might help. Best wishes, Saroj On Sun, July 1, 2007 1:07 pm, ssls sddd wrote: > Dear List, > > > I have a problem with using ReadAffy() on a server. I don't have such > problem when running on a stand-alone PC machine. Please help. Thanks! > > > Sincerely, > > > Alex > > > > > > > The code I ran: > > > library(affy) mydata <- ReadAffy() > > The error message is attached: > > >> library(affy) > Loading required package: Biobase > Loading required package: tools > > > Welcome to Bioconductor > > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Loading required package: reposTools > > > Attaching package: 'reposTools' > > > > The following object(s) are masked from package:Biobase : > > > note, userQuery > >> mydata <- ReadAffy() > Error in validObject(.Object) : invalid class "AffyBatch" object: > sampleNames different from names of phenoData rows In addition: Warning > messages: > 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead > 2: The phenoData class is deprecated, use AnnotatedDataFrame (with > ExpressionSet) instead > 3: The exprSet class is deprecated, use ExpressionSet instead > 4: The exprSet class is deprecated, use ExpressionSet instead > 5: The exprSet class is deprecated, use ExpressionSet instead > 6: The exprSet class is deprecated, use ExpressionSet instead > 7: The exprSet class is deprecated, use ExpressionSet instead > 8: The exprSet class is deprecated, use ExpressionSet instead > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >